X[0] = X[0][..., :10] # CO
X[1] = X[1][..., :10] # Xe
X = pp.interpolate_and_crop(X, real_dim)
pp.add_norm(X)
X = [x[:, :80, 8:80] for x in X]
return X
X_slices = [0, 5, 9] # Which AFM slices to plot
tip_names = ['CO', 'Xe'] # AFM tip types
fontsize = 20
# Initialize OpenCL environment on GPU
env = oclu.OCLEnvironment(i_platform=0)
FFcl.init(env)
oclr.init(env)
afmulator_args = {
'pixPerAngstrome':
20,
'lvec':
np.array([[0.0, 0.0, 0.0], [22.0, 0.0, 0.0], [0.0, 22.0, 0.0],
[0.0, 0.0, 7.0]]),
'scan_dim': (104, 96, 20),
'scan_window': ((2.0, 2.0, 7.0), (15.0, 14.0, 9.0)),
'amplitude':
1.0,
'df_steps':
10,
def construct_generator(molecules,
PPMdir,
Ymode='D-S-H',
batch_size=30,
nBestRotations=20,
scan_dim=(128, 128, 30),
nRot=100,
pixPerAngstrome=5,
Qs=[-0.1],
iZPPs=[8],
tip_type='quadrupole',
tipZs=None,
tipQs=None,
rot_tolerance=5,
Yrange=2,
distAbove=7.5,
distAboveDelta=None,
molCentering='box',
Rpp=-0.5,
dzmax=1.2,
dzmax_s=1.2,
diskMode='sphere',
zmin=-1.5,
zmin_xyz=-2.0,
Nmax_xyz=30,
shuffle_rotations=True,
shuffle_molecules=True,
preName='../Molecules/',
postName='.xyz',
maxTilt0=0.0,
wz=1.0,
df_weight_steps=10,
dz=0.1,
randomize_enabled=True,
randomize_parameters=False,
randomize_tip_tilt=True,
randomize_distance=True,
rndQmax=0.1,
rndRmax=0.2,
rndEmax=0.5,
rndAlphaMax=0.1,
rotations=None,
Rfunc=None,
invStep=None,
Rmax=None,
lvec=np.array([[0.0, 0.0, 0.0], [30.0, 0.0, 0.0],
[0.0, 30.0, 0.0], [0.0, 0.0, 30.0]])):
# ============ Setup Probe Particle
if not isinstance(Qs, list):
Qs = [Qs]
if not isinstance(iZPPs, list):
iZPPs = [iZPPs]
sys.path.append(PPMdir)
import pyopencl
import pyProbeParticle.common as PPU
import pyProbeParticle.GeneratorOCL_LJC as PPGen
import pyProbeParticle.oclUtils as oclu
# Initialize OpenCL kernels and stuff
try:
env = oclu.OCLEnvironment(i_platform=0)
PPGen.FFcl.init(env)
PPGen.oclr.init(env)
except pyopencl.cffi_cl.RuntimeError as e:
print('Environment could not be initialized. Maybe already was.')
print('Error:')
print(e)
if rotations is None:
# Make rotations
rotations = PPU.sphereTangentSpace(
n=nRot) # http://blog.marmakoide.org/?p=1
# Make data generator
data_generator = PPGen.Generator(molecules,
rotations,
batch_size,
pixPerAngstrome=pixPerAngstrome,
Ymode=Ymode)
# Handle tip types
if tip_type == 'monopole':
if tipZs is None:
tipZs = [0, 0, 0, 0]
if tipQs is None:
tipQs = [1, 0, 0, 0]
elif tip_type == 'dipole':
if tipZs is None:
tipZs = [0.1, -0.1, 0, 0]
if tipQs is None:
tipQs = [10, -10, 0, 0]
elif tip_type == 'quadrupole':
if tipZs is None:
tipZs = [0.1, 0, -0.1, 0]
if tipQs is None:
tipQs = [100, -200, 100, 0]
else:
raise ValueError(
"Got tip_type %s. Should be 'monopole', 'dipole', or 'quadrupole'."
% str(tip_type))
# Set probe particle(s)
tipZs = np.array(tipZs)
tipQs = np.array(tipQs)
data_generator.bQZ = True
data_generator.iZPPs = iZPPs
data_generator.QZs = [tipZs for _ in range(len(Qs))]
data_generator.Qs = [q * tipQs for q in Qs]
data_generator.rot_tolerance = rot_tolerance
if data_generator.projector is not None:
data_generator.projector.Rpp = Rpp
data_generator.projector.dzmax = dzmax
data_generator.projector.dzmax_s = dzmax_s
data_generator.projector.zmin = zmin
data_generator.projector.Rfunc = Rfunc
data_generator.projector.invStep = invStep
data_generator.projector.Rmax = Rmax
data_generator.preName = preName
data_generator.postName = postName
data_generator.scan_dim = scan_dim
data_generator.nBestRotations = nBestRotations
data_generator.shuffle_rotations = shuffle_rotations
data_generator.shuffle_molecules = shuffle_molecules
data_generator.Yrange = Yrange
data_generator.lvec = lvec
data_generator.distAbove = distAbove
data_generator.distAboveDelta = distAboveDelta
data_generator.molCentering = molCentering
data_generator.molCenterAfm = True
data_generator.maxTilt0 = maxTilt0
data_generator.zmin_xyz = zmin_xyz
data_generator.Nmax_xyz = Nmax_xyz
data_generator.diskMode = diskMode
# --- 'MultiMapSpheres' settings ztop[ichan] = (R - Rmin)/Rstep
data_generator.nChan = 3 # number of channels, resp. atom size bins
data_generator.Rmin = 1.4 # minimum atom radius
data_generator.Rstep = 0.2 # size range per bin (resp. channel)
# Params randomization
data_generator.randomize_enabled = randomize_enabled
data_generator.randomize_tip_tilt = randomize_tip_tilt
data_generator.randomize_parameters = randomize_parameters
data_generator.randomize_distance = randomize_distance
data_generator.rndQmax = rndQmax # charge += rndQmax * ( rand()-0.5 ) (negative is off)
data_generator.rndRmax = rndRmax
data_generator.rndEmax = rndEmax
data_generator.rndAlphaMax = rndAlphaMax
# z-weight exp(-wz*z)
data_generator.wz = wz
data_generator.zWeight = data_generator.getZWeights()
# Weight function for Fz -> df conversion ( oscillation amplitude 1.0Angstroem = 10 * 0.1 ( 10 n steps, dz=0.1 Angstroem step lenght ) )
dfWeight = PPU.getDfWeight(df_weight_steps, dz=dz)[0].astype(np.float32)
data_generator.dfWeight = dfWeight
data_generator.initFF()
return data_generator